[BioC] KEGG2heatmap - blank rows

[Saroj K Mohapatra]

Hi Lavinia:

Lavinia Gordon wrote:
>    foo <- KEGG2heatmap("04810", sample.ExpressionSet, "hgu95av2")
>    > foo
>    $rowInd
>     [1]  2  9  4  6  7  8  3  5  1 10
>   
This is in keeping with the fact that there are 10 common probe sets 
between the pathway selected and the sample data you used in this example.

 > probeids=get("04810", hgu95av2PATH2PROBE)
 > intersect(probeids,featureNames(sample.ExpressionSet))
 [1] "AFFX-HSAC07/X00351_3_at" "AFFX-HSAC07/X00351_3_st"
 [3] "AFFX-HSAC07/X00351_5_at" "AFFX-HSAC07/X00351_5_st"
 [5] "AFFX-HSAC07/X00351_M_at" "AFFX-HSAC07/X00351_M_st"
 [7] "31719_at"                "31720_s_at"            
 [9] "31699_at"                "31557_at"              

>    $colInd
>     [1] 13 24 17 19 10  4 26  6  7  2 16 11  9 23 14 25 12  8 15 22 21 18 20
>    1  3  5
>    $Rowv
>    NULL
>    $Colv
>    NULL
>    What  does  foo$rowInd  refer  to?  I have checked these indexes in my
>    ExpressionSet and in the chip data and none of the returned probe names
>    appear on the heatmap.
>   
It refers to the index of the probe set id (among the 10) after 
reordering. On the heatmap, if you start from the bottom, the first 
probe set is "AFFX-HSAC07/X00351_3_st", which is the second one on the 
list of 10 that I showed above. The second probe set on the heatmap is 
"31699_at", which is the 9th one on the list, and so on.

Hope that helps.

Saroj

>    with regards
>    Lavinia Gordon.
>    > sessionInfo()
>    R version 2.9.0 (2009-04-17)
>    i386-pc-mingw32
>    locale:
>    LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETAR
>    Y=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252
>    attached base packages:
>    [1] grid      stats     graphics  grDevices utils     datasets  methods
>    base
>    other attached packages:
>     [1]      KEGG.db_2.2.11           SPIA_1.0.0              RCurl_1.2-0
>    RColorBrewer_1.0-2  gplots_2.7.1        caTools_1.9
>     [7]      bitops_1.0-4.1          gdata_2.6.1             gtools_2.6.1
>    annotate_1.22.0     chicken.db_2.2.11   RSQLite_0.7-3
>    [13]      DBI_0.2-4               AnnotationDbi_1.6.1     gcrma_2.16.0
>    Biostrings_2.12.10  IRanges_1.2.3       affy_1.22.1
>    [19] Biobase_2.4.1       limma_2.18.3
>    loaded via a namespace (and not attached):
>    [1]     affyio_1.12.0            preprocessCore_1.6.0    splines_2.9.0
>    xtable_1.5-5
>
>    Lavinia Gordon
>    Research Officer
>    Bioinformatics
>    Murdoch Childrens Research Institute
>    Royal Children's Hospital
>    Flemington Road Parkville Victoria 3052 Australia
>    telephone: +61 3 8341 6221
>    [1]www.mcri.edu.au
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